Hematologic Cancer after Gene Therapy for Cerebral Adrenoleukodystrophy

Large-scale discovery of potent, compact and erythroid specific enhancers for gene therapy vectors

Gene expression during cell development and differentiation is orchestrated by distal regulatory elements that precisely modulate cell selective gene activity. Gene therapy vectors leverage these elements for precise spatiotemporal transgene expression. Here, we develop a one-shot approach to screen candidate regulatory sequences from large-scale epigenomics data for programmable transgene expression within gene therapy viral vectors. We assess a library of 15,000 short sequences derived from developmentally active elements during erythropoiesis using a clinically relevant reporter vector. These elements display a gradient of transcriptional enhancer activity in erythroid cells, with high cell type restriction and developmental stage specificity. Finally, replacing the canonical β-globin μLCR with a compact enhancer in a β-thalassemia lentiviral vector successfully corrects the thalassemic phenotype in patient-derived hematopoietic and stem and progenitor cells (HSPCs), while increasing viral titers and cell transducibility. Our approach provides further insights into enhancer biology with wider implications for human gene therapy.

Gene regulation technologies for gene and cell therapy

Gene therapy stands at the forefront of medical innovation, offering unique potential to treat the underlying causes of genetic disorders and broadly enable regenerative medicine. However, unregulated production of therapeutic genes can lead to decreased clinical utility due to various complications. Thus, many technologies for controlled gene expression are under development, including regulated transgenes, modulation of endogenous genes to leverage native biological regulation, mapping and repurposing of transcriptional regulatory networks, and engineered systems that dynamically react to cell state changes. Transformative therapies enabled by advances in tissue-specific promoters, inducible systems, and targeted delivery have already entered clinical testing and demonstrated significantly improved specificity and efficacy. This review highlights next-generation technologies under development to expand the reach of gene therapies by enabling precise modulation of gene expression. These technologies, including epigenome editing, antisense oligonucleotides, RNA editing, transcription factor-mediated reprogramming, and synthetic genetic circuits, have the potential to provide powerful control over cellular functions. Despite these remarkable achievements, challenges remain in optimizing delivery, minimizing off-target effects, and addressing regulatory hurdles. However, the ongoing integration of biological insights with engineering innovations promises to expand the potential for gene therapy, offering hope for treating not only rare genetic disorders but also complex multifactorial diseases.

Current and future treatments for sickle cell disease: From hematopoietic stem cell transplantation to in vivo gene therapy

Sickle cell disease (SCD) is a single-gene disorder caused by a point mutation of the β-globin gene, resulting in hemolytic anemia, acute pain, multiorgan damage, and early mortality. Hydroxyurea is a first-line drug therapy that switches sickle-globin to non-pathogenic γ-globin; however, it requires lifelong oral administration. Allogeneic hematopoietic stem cell (HSC) transplantation allows for a one-time cure for SCD, albeit with histocompatibility limitations. Therefore, autologous HSC gene therapy was developed to cure SCD in a single treatment, without HSC donors. Current HSC gene therapy is based on the ex vivo culture of patients' HSCs with lentiviral gene addition and gene editing, followed by autologous transplantation back to the patient. However, the complexity of the treatment process and high costs hinder the universal application of ex vivo gene therapy. Therefore, the development of in vivo HSC gene therapy, where gene therapy tools are directly administered to patients, is desirable to provide a more accessible, cost-effective solution that can cure SCD worldwide. In this review, we discuss current treatments, including drug therapies, HSC transplantation, and ex vivo gene therapy; the development of gene therapy tools; and progress toward curative in vivo gene therapy in SCD.

Gene therapy for hemophilia - From basic science to first approvals of "one-and-done" therapies

Realistic paths to gene therapy for the X-linked bleeding disorder hemophilia started to materialize in the mid 1990s, resulting in disease correction in small and large animal models. Out of a diversity of approaches, in vivo adeno-associated viral (AAV) gene transfer to hepatocytes emerged as the most promising strategy, eventually forming the basis for multiple advanced clinical trials and regulatory approval of two products for the treatment of hemophilia B (coagulation factor IX deficiency) and one for hemophilia A (factor VIII deficiency). Ideally, gene therapy is effective with a single administration, thus providing therapeutic factor levels over a period of years, without the need for frequent injections. Overcoming multiple obstacles, some not predicted by preclinical studies, sustained partial to complete correction of coagulation for several years to an entire decade has now been documented in patients, with observation ongoing. A hyperactive form of FIX improved efficacy in hemophilia B, and superior engineered variants of FVIII are emerging. Nonetheless, challenges remain, including pre-existing immunity to AAV capsids, toxicities, inter-patient variability in response to treatment, and difficulty in obtaining durable therapeutic expression of FVIII. In alternative approaches, in vivo gene editing and ex vivo gene therapies targeting hemopoietic cells are in development.

Ex vivo modification of hematopoietic stem and progenitor cells for gene therapy

The development of viral vectors has been particularly critical for genetic therapies of hematological diseases. Before the development of retrovirus vectors (RVVs), gene transfer into mammalian cells was accomplished by transduction of DNA plasmids by chemical means and later by electroporation. The main limitation of these methods is the inefficiency of transfer of intact sequences, and particularly with electroporation significant cell death of the manipulated cells. The earliest successful human gene therapy trials utilized γ-RVVs and many of the techniques developed in the 1980s. A breakthrough for the field was the exploitation and development of HIV for transfer vectors, termed lentivirus vectors. In this review, we highlight uses of retro- and lentivirus vectors in monogenic diseases in which hematopoietic stem cells are used in the autologous setting to treat immunodeficiencies, hemoglobinopathies and metabolic diseases. The three authors' perspective represent experiences in the field over four decades that encompasses both basic translational research and development and oversight of early and ongoing gene therapy trials utilizing viral vectors.

Opportunities and Challenges of Fetal Gene Therapy

OBJECTIVE

Fetal gene therapy represents a promising approach to treat severe congenital disorders by intervening during a critical developmental period. This review aims to explore the unique advantages, specific applications, and challenges of this early intervention strategy.

METHOD

We reviewed preclinical and emerging clinical studies evaluating the biological rationale, feasibility, and therapeutic potential of gene therapy administered in utero.

RESULTS

The fetal window offers unique advantages, including enhanced tissue accessibility and biodistribution, immune tolerance to new therapeutic molecules, and has the potential to prevent irreversible organ damage before birth. However, this approach requires ethical considerations including risks to both the fetus and mother, complexities of informed consent, and broad societal implications.

CONCLUSION

Although substantial challenges remain, fetal gene therapy has the potential to improve outcomes in early-onset severe disorders that currently lack effective postnatal treatments.

Blood Biomarkers Reflecting Brain Pathology-From Common Grounds to Rare Frontiers

Understanding pathological changes in the brain is essential for guiding treatment decisions in brain injuries and diseases. Despite significant advances in brain imaging techniques, clinical practice still faces challenges due to infrastructure reliance and high resource demands. This review explores the current knowledge on blood-based biomarkers that indicate brain pathology, which can assist in identifying at-risk patients, diagnosing patients, predicting disease progression, and treatment response. We focus on the inherited metabolic disorders X-linked adrenoleukodystrophy (X-ALD) and metachromatic leukodystrophy (MLD) which share remarkable phenotypic variability. Disease-specific increases in the lipid metabolites lyso-PC26:0 in X-ALD and sulfatides in MLD might contribute to predicting clinical manifestation. Disease-unspecific biomarkers for axonal damage (neurofilament light chain protein, NfL) and glial degeneration (glial fibrillary acidic protein, GFAP) are able to distinguish X-ALD and MLD phenotypes at the group level. The implementation of X-ALD into newborn screening programs in various countries, including several U.S. states, has increased the demand for predictive blood-based biomarkers capable of detecting the early conversion from the pre-symptomatic to the early neuroinflammatory cerebral form of X-ALD. Among different biomarkers, NfL has proven most effective in reflecting neuroinflammation and correlating with brain lesion volume and the magnetic resonance imaging (MRI)-based severity scores. We discuss how NfL has moved from initial proof-of-principle towards proof-of-concept studies in brain disorders such as multiple sclerosis and how this knowledge could be applied for the clinical implementation of NfL in rare inherited metabolic disorders such as X-ALD.

Long-Term Effects of Atidarsagene Autotemcel for Metachromatic Leukodystrophy

BACKGROUND

Metachromatic leukodystrophy (MLD) is an ultrarare, severe lysosomal storage disorder caused by a deficiency of arylsulfatase A (ARSA).

METHODS

We treated patients who had MLD with atidarsagene autotemcel (arsa-cel), a hematopoietic stem-cell-based gene therapy, in two prospective open-label clinical studies and expanded-access programs. We compared their outcomes with those of untreated patients (natural history cohort). The primary end point was survival free from severe motor impairment (the time from birth to the first occurrence of loss of locomotion and of sitting without support or death from any cause).

RESULTS

A total of 39 treated patients and 49 untreated patients were included. The median follow-up was 6.76 years (range, 0.64 to 12.19). Arsa-cel resulted in a significantly lower risk of severe motor impairment or death than no treatment among patients with presymptomatic late-infantile MLD (P<0.001), those with presymptomatic early-juvenile MLD (P = 0.04), and those with early-symptomatic early-juvenile MLD (P<0.001). The estimated percentage of patients surviving without severe motor impairment at 6 years of age was 0% (95% confidence interval [CI], not evaluable) among untreated patients with late-infantile MLD and 100% (95% CI, 100 to 100) among treated patients with presymptomatic late-infantile MLD. The estimated percentage of patients surviving without severe motor impairment at 10 years of age was 11.2% (95% CI, 0.9 to 36.4) among untreated patients with early-juvenile MLD and 87.5% (95% CI, 38.7 to 98.1) and 80.0% (95% CI, 40.9 to 94.6) among treated patients with presymptomatic and early-symptomatic early-juvenile MLD, respectively. No evidence of insertional oncogenesis was found. The most common grade 3 or higher adverse event was febrile neutropenia. Anti-ARSA antibodies were detected transiently in 6 of 39 patients (15%). Three deaths occurred, all of which were considered by the investigators to be unrelated to arsa-cel.

CONCLUSIONS

Among patients with presymptomatic late-infantile or early-juvenile MLD and those with early-symptomatic early-juvenile MLD, the risk of severe motor impairment or death was significantly lower among those who received treatment with arsa-cel than in a natural history cohort that did not receive treatment. (Funded by Orchard Therapeutics and others; ClinicalTrials.gov numbers, NCT01560182 and NCT03392987.).

Clinical hematopoietic stem cell-based gene therapy

Hematopoietic stem cell (HSC)-based gene therapies have seen extraordinary progress since their initial conception, now fundamentally transforming the treatment paradigms for various inherited hematologic, immunologic, and metabolic conditions-with additional use cases under exploration. Decades worth of work with advances in viral vector technologies and cell manufacturing have paved the way for HSC gene therapy with marked improvement in the safety and efficiency of gene delivery into HSCs. These have been augmented by the recent rise of innovative genome-editing techniques, particularly using clustered regularly interspaced short palindromic repeats CRISPR-associated proteins (CRISPR-Cas)-based technologies, which have enabled more precise and reproducible genome alterations in HSCs and fostered opportunities for targeted gene modification or gene correction. These breakthroughs have led to the development of many active clinical trials and culminated in the recent federal regulatory-agency approvals of multiple clinical HSC gene therapies for various indications that are now becoming available across different geographies. These treatments aim to offer significant, long-lasting benefits to patients worldwide without the toxicities of alternative treatment approaches. This review explores the history and advancements in HSC gene therapies and provides a comprehensive overview of the latest clinical innovations and cell-therapy products. Further, it concludes with a discussion of the persistent challenges that have limited adoption and potential future opportunities that aspire to enable curative treatment of many different patients through such personalized medicines.

Treatment of leukodystrophies: Advances and challenges

Leukodystrophies, a group of genetic disorders primarily affecting brain white matter, were once considered untreatable. Advances in MRI and genetic diagnostics now allow most patients to receive a genetic diagnosis, and emerging treatments are shifting the field from therapeutic nihilism to cautious optimism. Allogenic haematopoietic stem cell transplantation (HSCT), used since the 1980s, has shown efficacy in specific leukodystrophies, such as adrenoleukodystrophy and metachromatic leukodystrophy, when administered early. Gene therapy has become a viable option, with ex vivo approaches like atidarsagene autotemcel providing promising outcomes for early-onset MLD. Trials for gene replacement and antisense oligonucleotide therapies are ongoing for several leukodystrophies, including Canavan disease and Alexander disease. Certain treatments, such as guanabenz for Vanishing White Matter, target disease-specific dysregulated molecular pathways. Despite these advances, challenges remain, including the ultrarare nature of most leukodystrophies, limited natural history data, high treatment costs, and barriers to accessibility. Future developments, including newborn screening and close international collaboration, aim to enhance early diagnosis, refine treatment timing, and expand access to innovative therapies.

Meta-Analysis and Optimization of the In Vitro Immortalization Assay for Safety Assessment of Retroviral Vectors in Gene Therapy

The underlying risk of retroviral vector-induced insertional oncogenesis in gene therapies requires a reliable preclinical safety assessment. Dysregulation of genes neighboring the vector's integration sites has triggered hematopoietic malignancies in patients treated with different vector genera and designs. With ca. 18 years in practical use, the in vitro immortalization (IVIM) assay can quantify this mutagenic potential and is actively requested by regulatory authorities during preclinical stages. Here, we present a thorough meta-analysis of IVIM data alongside a step-by-step cell culture protocol. On this basis, we propose clonal outgrowth as the single indicator of mutagenicity, simplifying the IVIM assay cost- and time-wise.

Current landscape of vector safety and genotoxicity after hematopoietic stem or immune cell gene therapy

Malignant transformation of gene modified haematopoietic stem cells caused anxiety following adverse events in early clinical trials using gamma-retroviral vectors (γRV) to correct haematopoietic stem cells (HSC) in monogenic immune disorders. Adoption of HIV-derived lentiviral vectors (LV) with SIN (self-inactivating) configurations greatly reduced risks and subsequently hundreds of patients have been dosed with HSC gene therapy for blood, immune and metabolic conditions. Nevertheless, as experience builds, it's now well recognised that vector integration can drive clonal expansions and these may carry long term safety risks. Documented cases of haematological malignancy after SIN-LV gene therapy have recently emerged, in particular where heterologous retroviral promoters were employed and there are concerns around certain insulator elements and other possible contributors to clonal expansions. Similarly, tens of thousands of subjects have now received engineered T cell products, and longstanding dogma that mature T cells cannot be transformed is being questioned, with reports of a small number of malignant transformation events and wider concerns around secondary malignancies in some groups of patients. We summarize current clinical information and revisit genotoxicity risks following ex-vivo gene modification of HSC and T cells.

The bleeding edge: broadening horizons for hematopoietic stem cell therapies

Recent reports of gene therapy using autologous hematopoietic stem cell transplantation (HSCT) have addressed protein deficiencies of extra-hematopoietic origin. In a recent study, Srivastava et al. report that patients with hemophilia A receiving F8 lentiviral HSCT gene therapy achieved lasting factor VIII restoration and clinical improvement, marking an advance that could enable broader applications of HSCT.

Gene therapy for β-thalassemia: current and future options

Beta-thalassemia is a severe, hereditary blood disorder characterized by anemia, transfusion dependence, reduced life expectancy, and poor quality of life. Allogeneic transplantation of hematopoietic stem cells (HSCs) is the only curative treatment for transfusion-dependent β-thalassemia, but a lack of compatible donors prevents the use of this approach for most patients. Over the past 20 years, the rise of gene therapy and the development of lentiviral vectors and genome-editing tools has extended curative options to a broader range of patients. Here, we review breakthroughs in gene addition- and genome-editing-based therapies for β-thalassemia, the clinical outcomes enabling approval by regulatory agencies, and perspectives for further development.

Behavioral Abnormalities, Cognitive Impairments, Synaptic Deficits, and Gene Replacement Therapy in a CRISPR Engineered Rat Model of 5p15.2 Deletion Associated With Cri du Chat Syndrome

The Cri du Chat Syndrome (CdCS), a devastating genetic disorder caused by a deletion on chromosome 5p, faces challenges in finding effective treatments and accurate animal models. Using CRISPR-Cas9, a novel CdCS rat model with a 2q22 deletion is developed, mirroring a common genetic alteration in CdCS patients. This model exhibits pronounced deficits in social behavior, cognition, and anxiety, accompanied by neuronal abnormalities and immune dysregulation in key brain regions such as the hippocampus and medial prefrontal cortex (mPFC). The immunostaining and RNA-seq analyses provide new insights into CdCS pathogenesis, revealing inflammatory and immune processes. Importantly, it is demonstrated that early gene replacement therapy with AAV-Ctnnd2 alleviates cognitive impairments in CdCS rats, highlighting the potential for early intervention. However, the effectiveness of this therapy is confined to the early developmental stages and does not fully restore all CdCS symptoms. The findings deepen the understanding of CdCS pathogenesis and suggest promising therapeutic directions.

Ex vivo HIV DNA integration in STAT3 drives T cell persistence-A model of HIV-associated T cell lymphoma

Oncogenic retroviruses are known for their pathogenesis via insertional mutagenesis, in which the presence of a provirus and its transcriptional control elements alter the expression of a nearby or surrounding host gene. There are reports of proviral integration driving oncogenesis in people with HIV and the use of HIV-derived vectors for gene therapy has raised concern about oncogenic side effects. To study this issue, we used an ex vivo human CD4+ T cell infection model developed in our laboratory to identify HIV-1 integration sites that might influence cell proliferation or survival. Combining integration site analysis and bulk RNA sequencing, we established that an upregulated STAT3 signature due to proviral insertional mutagenesis was associated with persistent HIV-infected CD4+ T cells. HIV+ persistent cells also expressed a STAT3-related anti-apoptotic and cytotoxic phenotype that resembles that of HIV-associated T cell lymphomas. HIV insertional mutagenesis of STAT3 and expression of its downstream targets provides a model of HIV-associated T cell lymphomas that can be used to further determine the oncogenic drivers of HIV-associated lymphomas, both AIDS- and gene therapy-associated, and, potentially, to evaluate therapeutics against these HIV-associated cancers.

Author Summary

The effects of HIV proviral insertional mutagenesis have been demonstrated in a handful of HIV-associated T cell lymphomas, where integration of an HIV provirus within intron 1 of STAT3 , results in increased expression of the STAT3 protein. To study the effects of HIV insertional mutagenesis, we established an ex vivo culture protocol of primary human CD4+ T cells infected with a replication-incompetent HIV vector with a gfp-reporter. After infection, the HIV/GFP+ cells from all three donors declined, but, over time, 3/6 replicates from one donor populations of infected cells rebounded. The resurgent HIV/GFP+ cells contained a provirus integrated within intron 1 of STAT3 , which led to increases in gene expression, STAT3 activation, and upregulation of a STAT3 -associated anti-apoptotic and cytotoxic phenotype. The STAT3 -associated gene signature shared similarities to the HIV-associated lymphomas with similar integration sites. Additionally, in all 3 replicates, insertional mutagenesis of genes other than STAT3 may have also contributed to clonal expansion of HIV/GFP+ T cells. Overall, we have demonstrated that HIV provirus insertional mutagenesis can influence T cell persistence. Our study provides a primary T cell culture model system that can be used to further study how proviral insertional mutagenesis influences HIV-associated T cell lymphomas and the safety of lentiviral vectors used in gene and cell therapies.

The clinical landscape of CAR NK cells

Chimeric antigen receptor (CAR) NK cell therapy has emerged as a promising alternative to CAR T cell therapy, offering significant advantages in terms of safety and versatility. Here we explore the current clinical landscape of CAR NK cells, and their application in hematologic malignancies and solid cancers, as well as their potential for treating autoimmune disorders. Our analysis draws from data collected from 120 clinical trials focused on CAR NK cells, and presents insights into the demographics and characteristics of these studies. We further outline the specific targets and diseases under investigation, along with the major cell sources, genetic modifications, combination strategies, preconditioning- and dosing regimens, and manufacturing strategies being utilized. Initial results from 16 of these clinical trials demonstrate promising efficacy of CAR NK cells, particularly in B cell malignancies, where response rates are comparable to those seen with CAR T cells but with lower rates of severe adverse effects, such as cytokine release syndrome (CRS), immune effector cell-associated neurotoxicity syndrome (ICANS), and graft-versus-host disease (GvHD). However, challenges remain in solid tumor applications, where only modest efficacy has been observed to date. Our analysis reveals that research is increasingly focused on enhancing CAR NK cell persistence, broadening their therapeutic targets, and refining manufacturing processes to improve accessibility and scalability. With recent advancements in NK cell engineering and their increased clinical applications, CAR NK cells are predicted to become an integral component of next-generation immunotherapies, not only for cancer but potentially for immune-mediated diseases as well.

Population-scale cellular GUIDE-seq-2 and biochemical CHANGE-seq-R profiles reveal human genetic variation frequently affects Cas9 off-target activity

Genome editing enzymes can introduce targeted changes to the DNA in living cells 1-4 , transforming biological research and enabling the first approved gene editing therapy for sickle cell disease 5 . However, their genome-wide activity can be altered by genetic variation at on- or off-target sites 6-8 , potentially impacting both their precision and therapeutic safety. Due to a lack of scalable methods to measure genome-wide editing activity in cells from large populations and diverse target libraries, the frequency and extent of these variant effects on editing remains unknown. Here, we present the first population-scale study of how genetic variation affects the cellular genome-wide activity of CRISPR-Cas9, enabled by a novel, sensitive, and unbiased cellular assay, GUIDE-seq-2 with improved scalability and accuracy compared to the original broadly adopted method 9 . Analyzing Cas9 genome-wide activity at 1,115 on- and off-target sites across six guide RNAs in cells from 95 individuals spanning four genetically diverse populations, we found that variants frequently overlap off-target sites, with 13% significantly altering Cas9 editing activity by up to 33% indels. To understand common features of high-impact variants, we developed a new massively parallel biochemical assay, CHANGE-seq-R, to measure Cas9 activity across millions of mismatched target sites, and trained a deep neural network model, CHANGE-net, to accurately predict and interpret the effects of single-nucleotide variants on off-targets with up to six mismatches. Taken together, our findings illuminate a path to account for genetic variation when designing genome editing strategies for research and therapeutics.

T-cell neoplasias and secondary malignancies after CAR-T cell therapy: current knowledge, risk factors, and implications from CAR-T engineering strategies

Widespread use of CAR-T cell therapies for treatment of B cell malignancies has resulted in a frameshift in treatment strategies and improved patient outcomes since the first CAR-T product was FDA approved in 2017. Currently over 30,000 patients have been treated with approved CAR-T cell products, with many more likely to be treated in future, both as standard of care therapy as well as on clinical trials. As more patients are treated, development of rare complications has begun to emerge, and the incidence of second primary malignancies after CAR-T cell therapy is evolving from a hypothetical to a realized concern. Furthermore, in November 2023, the FDA issued a warning regarding the potential for CAR-T cell-derived T cell neoplasias to arise as a result of CAR-T manufacturing. Here we review patient risk factors for development of second primary malignancies including T cell neoplasias, CAR-T engineering strategies that may increase this risk, and the current body of literature surrounding incidence of second primary malignancies and case reports of T cell neoplasias arising after CAR-T cell therapy.

Role of B-Cell Lymphoma/Leukemia 11A in Normal and Malignant Hematopoiesis

B-cell lymphoma/leukemia 11A (BCL11A) is a crucial transcriptional regulator, widely recognized for its role in controlling fetal hemoglobin and its potential as a gene therapy target for inherited hemoglobinopathies. Beyond this, recent studies have also highlighted its key role in the maturation and function of immune cells and erythrocytes, mediated through the regulation of various molecules during hematopoietic development. The dysregulation of BCL11A disrupts downstream molecular pathways, contributing to the development of several hematological malignancies, particularly leukemias. This review provides a comprehensive overview of the role of BCL11A in normal and malignant hematopoiesis, details the hematological disorders associated with its dysregulation and explores the current therapeutic strategies targeting this transcription factor.

CEBPA repression by MECOM blocks differentiation to drive aggressive leukemias

Acute myeloid leukemias (AMLs) have an overall poor prognosis with many high-risk cases co-opting stem cell gene regulatory programs, yet the mechanisms through which this occurs remain poorly understood. Increased expression of the stem cell transcription factor, MECOM, underlies one key driver mechanism in largely incurable AMLs. How MECOM results in such aggressive AML phenotypes remains unknown. To address existing experimental limitations, we engineered and applied targeted protein degradation with functional genomic readouts to demonstrate that MECOM promotes malignant stem cell-like states by directly repressing pro-differentiation gene regulatory programs. Remarkably and unexpectedly, a single node in this network, a MECOM-bound cis-regulatory element located 42 kb downstream of the myeloid differentiation regulator CEBPA, is both necessary and sufficient for maintaining MECOM-driven leukemias. Importantly, targeted activation of this regulatory element promotes differentiation of these aggressive AMLs and reduces leukemia burden in vivo, suggesting a broadly applicable differentiation-based approach for improving therapy.

T-cell lymphomas in recipients of CAR-T cells: assessing risks and causalities

ABSTRACT

The US Food and Drug Administration announcement in November 2023 regarding reports of the occurrence of secondary T-cell lymphomas in patients receiving chimeric antigen receptor T cells (CAR-Ts) for B-cell malignancies resulted in widespread concern among patients, clinicians, and scientists. Little information relevant to assessing causality, most importantly whether CAR retroviral or lentiviral vector genomic insertions contribute to oncogenesis, was initially available. However, since that time, several publications have provided clinical and molecular details on 3 cases showing clonal CAR vector insertions in tumor cells but without firm evidence these insertions played any role in oncogenic transformation. In addition, several other cases have been reported without vector detected in tumor cells. In addition, epidemiologic analyses as well as institutional long-term CAR-T recipient cohort studies provide important additional information suggesting the risk of T-cell lymphomas after CAR-T therapies is extremely low. This review will provide a summary of information available to date, as well as review relevant prior research suggesting a low susceptibility of mature T cells to insertional oncogenesis and documenting the almost complete lack of T-cell transformation after natural HIV infection. Alternative factors that may predispose patients treated with CAR-Ts to secondary hematologic malignancies, including immune dysfunction and clonal hematopoiesis, are discussed, and likely play a greater role than insertional mutagenesis in secondary malignancies after CAR therapies.

The Newborn Screening Programme Revisited: An Expert Opinion on the Challenges of Rett Syndrome

Genomic sequencing has the potential to revolutionise newborn screening (NBS) programmes. In 2024, Genomics England began to recruit for the Generation Study (GS), which uses whole genome sequencing (WGS) to detect genetic changes in 500 genes in more than 200 rare conditions. Ultimately, its purpose is to facilitate the earlier identification of rare conditions and thereby improve health-related outcomes for individuals. The adoption of rare conditions into the GS was guided by four criteria: (1) the gene causing the condition can be reliably detected; (2) if undiagnosed, the rare condition would have a serious impact; (3) early or presymptomatic testing would substantially improve outcomes; and (4) interventions for conditions screened are accessible to all. Rett syndrome (RTT, OMIM 312750), a paediatric neurodevelopment disorder, was not included in the list of rare conditions in the GS. In this opinion article, we revisit the GS and discuss RTT from the perspective of these four criteria. We begin with an introduction to the GS and then summarise key points about the four principles, presenting challenges and opportunities for individuals with RTT. We provide insight into how data could be collected during the presymptomatic phase, which could facilitate early diagnosis and improve our understanding of the prodromal stage of RTT. Although many features of RTT present a departure from criteria adopted by the GS, advances in RTT research, combined with advocacy from parent-based organisations, could facilitate its entry into future newborn screening programmes.

Long-term tracking of haematopoietic clonal dynamics and mutations in non-human primate undergoing transplantation of lentivirally barcoded haematopoietic stem and progenitor cells

Haematopoietic stem and progenitor cell (HSPC) autologous gene therapies are promising treatment for a variety of blood disorders. Investigation of the long-term HSPC clonal dynamics and other measures of safety and durability following lentiviral-mediated gene therapies in predictive models are crucial for assessing risks and benefits in order to inform decisions regarding wider utilization. We established an autologous lentivirally barcoded HSPC transplantation model in rhesus macaque (RM), a model offering insights into haematopoiesis and gene therapies with direct relevance to human. Healthy young adult RMs underwent total body irradiation, followed by transplantation of autologous HSPCs transduced with a lentiviral vector containing a diverse genetic barcode library, uniquely labelling individual HSPCs and their progeny. With up to 131 months of follow-up, we now report quantitative clonal dynamics, characterizing the number, diversity, stability and lineage bias of hundreds of thousands of HSPC clones tracked in five RMs. We documented long-term stable and multi-lineage output from a highly polyclonal pool of HSPCs. Clonal succession after stable haematopoietic reconstitution was minimal. There was no evidence for accelerated acquisition of acquired somatic mutations following autologous lentivirally transduced HSPC transplantation. Our results provide relevant insights into long-term HSPC behaviours in vivo following transplantation and gene therapies.

Identification of c.146G > A mutation in a Fabry patient and its correction by customized Cas9 base editors in vitro

Fabry disease (FD) is a rare X-linked lysosomal storage disorder caused by mutations in the GLA gene, leading to reduced α-galactosidase (α-Gal A) activity. Current treatments, like enzyme replacement, have limitations affecting efficacy and patient outcomes. CRISPR/Cas9 genome editing tools may offer the potential to develop therapeutic strategy via correcting GLA mutations. In this study, we diagnosed a female FD patient with a missense mutation in exon 1 of the GLA gene (c.146G > A, p.R49H). Bioinformatic predictions and biochemical analyses in GLA-knockout cells revealed that this mutation significantly reduced α-Gal A stability and activity, confirming its pathogenicity. To correct this, we used adenine base editing. The mutation, along with a nearby bystander A, was efficiently edited by the traditional N-terminal adenine base editor. To avoid unwanted bystander editing, we developed a series of domain-inlaid base editors with the aim of narrowing editing window. The most effective variant, with deaminase inserted between the 947th and 948th residues of the RUVC3 domain, was further optimized by modifying linker rigidity. These adjustments shifted the editing window, eliminating bystander editing. Our findings clarify the pathogenic nature of a novel GLA mutation and demonstrate the potential of a customized base editor for therapeutic application in FD.

Oligodendrocytes, the Forgotten Target of Gene Therapy

If the billions of oligodendrocytes (OLs) populating the central nervous system (CNS) of patients could express their feelings, they would undoubtedly tell gene therapists about their frustration with the other neural cell populations, neurons, microglia, or astrocytes, which have been the favorite targets of gene transfer experiments. This review questions why OLs have been left out of most gene therapy attempts. The first explanation is that the pathogenic role of OLs is still discussed in most CNS diseases. Another reason is that the so-called ubiquitous CAG, CBA, CBh, or CMV promoters-widely used in gene therapy studies-are unable or poorly able to activate the transcription of episomal transgene copies brought by adeno-associated virus (AAV) vectors in OLs. Accordingly, transgene expression in OLs has either not been found or not been evaluated in most gene therapy studies in rodents or non-human primates. The aims of the current review are to give OLs their rightful place among the neural cells that future gene therapy could target and to encourage researchers to test the effect of OL transduction in various CNS diseases.

Lentiviral Gene Therapy for Cerebral Adrenoleukodystrophy

BACKGROUND

Cerebral adrenoleukodystrophy is a severe form of X-linked adrenoleukodystrophy characterized by white-matter disease, loss of neurologic function, and early death. Elivaldogene autotemcel (eli-cel) gene therapy, which consists of autologous CD34+ cells transduced with Lenti-D lentiviral vector containing ABCD1 complementary DNA, is being tested in persons with cerebral adrenoleukodystrophy.

METHODS

In a phase 2-3 study, we evaluated the efficacy and safety of eli-cel therapy in boys with early-stage cerebral adrenoleukodystrophy and evidence of active inflammation on magnetic resonance imaging (MRI). The primary efficacy end point was survival without any of six major functional disabilities at month 24. The secondary end points included overall survival at month 24 and the change from baseline to month 24 in the total neurologic function score.

RESULTS

A total of 32 patients received eli-cel; 29 patients (91%) completed the 24-month study and are being monitored in the long-term follow-up study. At month 24, none of these 29 patients had major functional disabilities; overall survival was 94%. At the most recent assessment (median follow-up, 6 years), the neurologic function score was stable as compared with the baseline score in 30 of 32 patients (94%); 26 patients (81%) had no major functional disabilities. Four patients had adverse events that were directly related to eli-cel. Myelodysplastic syndrome (MDS) with excess blasts developed in 1 patient at month 92; the patient underwent allogeneic hematopoietic stem-cell transplantation and did not have MDS at the most recent follow-up.

CONCLUSIONS

At a median follow-up of 6 years after lentiviral gene therapy, most patients with early cerebral adrenoleukodystrophy and MRI abnormalities had no major functional disabilities. However, insertional oncogenesis is an ongoing risk associated with the integration of viral vectors. (Funded by Bluebird Bio; ALD-102 and LTF-304 ClinicalTrials.gov numbers NCT01896102 and NCT02698579, respectively.).